Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_001323289.2(CDKL5):c.2572C>T (p.Arg858Cys)

CA10360567

426292 (ClinVar)

Gene: CDKL5 (HGNC:6792)
Condition: CDKL5 disorder (MONDO:0100039)
Inheritance Mode: X-linked inheritance
UUID: 0d082eec-a176-45ad-a6c0-b5ba2d32a963
Approved on: 2026-01-28
Published on: 2026-06-26

HGVS expressions

NM_001323289.2(CDKL5):c.2572C>T (p.Arg858Cys)
NM_001323289.2:c.2572C>T
NC_000023.11:g.18628446C>T
CM000685.2:g.18628446C>T
NC_000023.10:g.18646566C>T
CM000685.1:g.18646566C>T
NC_000023.9:g.18556487C>T
NG_008475.1:g.207842C>T
ENST00000623535.2:c.2572C>T
ENST00000674046.1:c.2695C>T
ENST00000379989.6:c.2572C>T
ENST00000379996.7:c.2572C>T
ENST00000623535.1:c.2572C>T
NM_001037343.1:c.2572C>T
NM_003159.2:c.2572C>T
NM_001323289.1:c.2572C>T
NM_001037343.2:c.2572C>T
NM_003159.3:c.2572C>T
More

Benign

Met criteria codes 3
BP5_Strong BS2 BS1
Not Met criteria codes 1
PP3

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Rett and Angelman-like Disorders Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for CDKL5 Version 5.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Rett and Angelman-like Disorders VCEP
The highest population minor allele frequency of the p.Arg858Cys variant in CDKL5 in gnomAD v4.1 is 0.00004538 in the Ashkenazi Jewish population, which is higher than the ClinGen Rett and Angelman-like Disorders VCEP threshold (≥0.0000083) for BS1, and therefore meets this criterion (BS1). The p.Arg858Cys variant is observed in at least 2 unaffected individuals (GeneDx- internal database) (BS2). The p.Arg858Cys variant is found in at least 3 patients with an alternate molecular basis of disease (Labcorp Genetics (formerly Invitae)- internal database; GeneDx- internal database) (BP5_Strong). Computational prediction analysis tools are inconclusive for this variant. In summary, the p.Arg858Cys variant in CDKL5 is classified as benign based on the ACMG/AMP criteria (BS1, BS2, BP5_Strong). (CDKL5 Specifications v.5.0; curation approved on 01/28/2026)
Met criteria codes
BP5_Strong
The p.Arg858Cys variant is found in at least 3 patients with an alternate molecular basis of disease (Labcorp Genetics (formerly Invitae)- internal database; GeneDx- internal database) (BP5_Strong).
BS2
The p.Arg858Cys variant is observed in at least 2 unaffected individuals (GeneDx- internal database) (BS2).
BS1
The highest population minor allele frequency of the p.Arg858Cys variant in CDKL5 in gnomAD v4.1 is 0.00004538 in the Ashkenazi Jewish population, which is higher than the ClinGen Rett and Angelman-like Disorders VCEP threshold (≥0.0000083) for BS1, and therefore meets this criterion (BS1).
Not Met criteria codes
PP3
Computational prediction analysis tools are inconclusive for this variant.
Curation History
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